wrong higher categories on Pensoft articles: how to deal with it

[myrmoteras]

@gsautter if we encounter wrong higher categories in Pensoft sourced journals, how to deal with this?
see eg plazi/community#136

1. If we notify Pensoft and they fix it, will this also be transferred to us?
2. If not, then we have to do it on our end.

[myrmoteras]

Looking at the pensoft XML, we are introducing them. so we need not only to correct this, but also have a policy how we add these attributes

[gsautter]

Right now, we take the higher taxa from the Pensoft TaxPub documents as what they are, simply assuming they are correct ... the idea is to not diverge from the original publication, but represent it as accurate as possible ... should we design a different approach?

[lyubomirpenev]

@t.georgiev please check the issue and report back. I believe you take the higher classification from our article-level metadata?

On 1/31/2022 2:37 PM, Guido Sautter wrote: Right now, we take the higher taxa from the Pensoft TaxPub documents as what they are, simply assuming they are correct ... the idea is to not diverge from the original publication, but represent it as accurate as possible ... should we design a different approach? — Reply to this email directly, view it on GitHub <#29 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABDFNGJVVQ64FYQ2QGTVRI3UYZ67ZANCNFSM5NAU4G2Q>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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[myrmoteras]

this is what we have in TB from https://zookeys.pensoft.net/article/78233/

<taxonomicName id="61E2AFA59755A493ECAB7982134B81E5" LSID="http://zoobank.org/A2EF195A-A19C-43CD-A774-A06218E96EE9" authority="sp. nov." authorityName="sp. nov." class="Mammalia" family="Soricidae" genus="Chodsigoa" higherTaxonomySource="CoL" kingdom="Animalia" lsidName="Chodsigoa dabieshanensis" order="Eulipotyphla" pageId="0" pageNumber="129" phylum="Chordata" rank="species" species="dabieshanensis">Chodsigoa dabieshanensis sp. nov.</taxonomicName>

https://tb.plazi.org/GgServer/xml/AFACD42EDC6C56578612A6C37DF62B8B

https://tb.plazi.org/GgServer/html/AFACD42EDC6C56578612A6C37DF62B8B

and that is what's in Zookeys

<tp:taxon-name> <object-id content-type="arpha">AFACD42E-DC6C-5657-8612-A6C37DF62B8B</object-id> <tp:taxon-name-part taxon-name-part-type="genus" reg="Chodsigoa">Chodsigoa</tp:taxon-name-part> <tp:taxon-name-part taxon-name-part-type="species" reg="dabieshanensis">dabieshanensis</tp:taxon-name-part> <object-id content-type="zoobank" xlink:type="simple">http://zoobank.org/A2EF195A-A19C-43CD-A774-A06218E96EE9</object-id> </tp:taxon-name>

and

<subj-group subj-group-type="biological_taxon"> <subject>Chordata</subject> <subject>Mammalia</subject> <subject>Soricidae</subject> <subject>Vertebrata</subject> </subj-group>

How does the higher categories get attributes in Plazi <taxonomicName> ?

What to do if there are errors or missing higher categories?

[gsautter]

For treatment taxa, the importer also considers the higher taxa given in the tp:treatment-meta/kwd-group element ... here the source TaxPub (https://zookeys.pensoft.net/article/78233/download/xml/):

The authority is most definitely wrong ... and the higher taxa in the TreatmentBank XML match the ones givem in the TaxPub.

[myrmoteras]

in this case, where does the phylum and class originate?

[gsautter]

in this case, where does the phylum and class originate?

Filled in from CoL and GBIF ... but existing higher taxa aren't replaced with these lookup results.

To ask the other way around: which higher taxa are wrong, exactly? If it's class and phylum, that's for me to investigate, but if it's others, the source TaxPub is the origin of those ...

[teodorgeorgiev]

It seems OK to me ... what exactly is wrong?

[gsautter]

@teodorgeorgiev <tp:taxon-authority>sp. nov.</tp:taxon-authority> doesn't really look right to me ... it's a status label, not an authority, is it?

[teodorgeorgiev]

Yes, the authority is wrong ... but I did not get what is wrong with the higher taxa

[gsautter]

Guess I'll have to check the higher taxa, then ... TB adds class and phylum to complete the higher taxa, so there might have been a mishap there.

[teodorgeorgiev]

it is corrected to tp:taxon-statussp. nov.</tp:taxon-status> ...

[gsautter]

it is corrected to tp:taxon-status>sp. nov.</tp:taxon-status> ...

OK, thanks, will re-import it asap.

[myrmoteras]

@teodorgeorgiev we fixed it- that's why there is not nothing wrong.

[teodorgeorgiev]

@gsautter @myrmoteras Thanks! I appreciate really that. Is there a problem with the higher categories or it was only the wrong authority?

[gsautter]

@teodorgeorgiev reading the above, seems as though the higher taxa might have been phylum and class only (added on our end), which @myrmoteras said was corrected, so the authority would have been the only error in the source TaxPub proper.

[teodorgeorgiev]

@gsautter all clear now, 10x!